The submission in this regard was made by CBI counsel before a division bench, comprising Chief Justice Manjula Chellur and Justice P R Ramachandra Menon.
The counsel said that the agency is willing to take up the investigation, considering the vulnerability situation of the children and inter-state ramifications of the case.
The bench, which described as 'shocking' the manner in which the young children were brought to kerala, observed that this was the first time CBI was coming forward to take up a case.
"We did not see any progress', the bench held while considering a PIL, seeking a CBI investigation into the case.
The bench did not permit impleading of Association of Orphanages in the case and said 'we are not against any orphanages and Association was showing over anxiety'.
"When matters relating to juvenile cases come up, the court has to act as guardian. The children are vulnerable and sensitive, who cannot speak for themselves. Somebody should take their responsibility", the bench said.
The bench also wanted to know if the children have parents and whether they were given voluntarily and if they were solicited from anyone from Kerala.
The case will be further considered on Friday.
Over 580 children from Bihar, Jharkhand and West Bengal, meant to be brought to two orphanages in the state, were detained by police at a railway station in Palakkad early in June after it was found many of them did not have any proper documents.
The issue had snowballed into a major row in the state with IUML, the key partner in UDF,taking objection to treating the incident as a case of child trafficking.
The children are now kept at state-run juvenile homes of the Child Welfare Society in Palakkad, Malappuram and Thrissur.
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